Sae is the Core, and hence is generally considered to be the "boss", as it is her mind. Therefore Sobe is forced to listen and obey if Sae gives her a direct command.
Control is taken by standing on the pedestal in the mindscape, which merges that consciousness into the body.
About Alters: The purpose of an alter is to hold memories that the Core is not ready to remember, and generally to aid the Core. An Alter cannot die unless killed/merged directly with the Core.
Senka: Senka is not a true alter in that she doesn't hold any memories to help Sae. Senka is what Sae *could* be when she merges with Sobe. However, her base personality has been corrupted by the destructive effects of Blue Magic. Because she is not a true alter, she does not listen to any orders given by Sae, and instead takes revenge by mentally torturing Sae and Sobe.
A crude picture of the Mindscape:

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